On 11/12/13 1:15 AM, arun kumar wrote:
Dear Gromacs users,
I am running a 50ns simulation of a protein having nearly 700 residues on
60 threads (Gromacs 4.6.3).
At one point i got a disk space problem, so i have deleted the md.trr file
and created an empty md.trr file. when i tried to restart the simulation
from check point file on 100 threads, [ mdrun -v -deffnm md -cpi md.cpt -nt
100 ]
i am getting a note and an error as fallows
Reading checkpoint file md.cpt generated:
#PME-nodes mismatch,
current program: 100
checkpoint file: 60
Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.
...
Source code file: checkpoint.c, line: 1767
Fatal error:
Can't read 1048576 bytes of 'md.trr' to compute checksum. The file
has been replaced or its contents has been modified.
please help me in overcoming this problem.
Use -noappend. If you mess with any of the files that mdrun produces, the file
appending procedure (which is the default behavior) will fail.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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